Originally posted by Mike Gene:Nic: Hey, I'm just following the peer-reviewed lit., man. Take it up in the pages of Biochemistry if you like...

The authors never claim MTH1022 is a homolog of motA. And even if they did, the claim would be unsupported.

People can read the quote I posted and decide for themselves exactly what the authors meant. Mentioning significant sequence similarity in the middle of a discussion of homologs seems like a strong indication to me that they meant homolog or at least "likely homolog". And see below for what some of those proteins are labeled as in the NCBI database.

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Actually, running a PSI-BLAST of ExbB gets me four hits on archaeabacteria, but whatever.

With e values of 0.005 and higher. That's not very impressive. Furthermore, even if there is a non-convergent and real relationship here, note that it is not widely distributed and would thus seem to have evolved long after archaea appeared.

A much stronger point is that the ExbB homologs are very widely distributed in eubacteria, in very basal lineages.

The distribution taxonomy report for ExbB is, in fact, rather like the taxonomy report for standard protein blast of E. coli's MotA protein: lots and lots of enterobacteria and proteobacteria, and a few hits out in spirochetes and other various deeply divergent bacteria.

Are we to conclude that MotA is just as likely to be of late origin and derived as ExbB?

...methinks the database may be a wee bit biased towards certain intensively-studied gram-negative bacteria groups and that therefore seeing many hits in those groups and few outside means very little in terms of relative significance. As I showed, you have to put MotA and ExbB in the same distribution bucket regardless.

Regarding low e-values:

Based on your blanket skepticism of marginal e-values, you may want to argue that some MotA proteins are of independent origins and convergent on standard MotA's. Many of these scores are non too impressive, yet some are MotAs (or PomA, a related motor) despite this:

These kinds of things ought to at least be mentioned and discussed before reckless statements are made about absolutely no evidence for precursors to flagellar proteins, that's my only point. For some reason you guys prefer to sweep it under the rug by unsupported arguments about ExbB's narrow distribution. Just acknowledge that this little bit of the biological world is a bit disharmonious with the flagellum-was-specially-created thesis. All I've been saying, and now documenting, is that ExbB homologs are at least as widely distributed as MotA, and possibly more widely distributed.